Fig. 3: The impact of Copy number alteration and mutations on mRNAs, proteins and phosphoproteins.

A The volcano plot indicated the arm level copy number alteration predictive of OS in gliomas. B The Venn plot depicted the cascading effects of copy number alterations (CNAs) of genes located on chromosome 7p. C The heatmap indicated the pathways enriched by the 123 cis effected proteins (right) and 201 cis effected mRNAs (left). The color of each cell showed −log₁₀ transformed p value (one-sided hypergeometric test). D The volcano plot indicated the 123 cis effected proteins predictive of OS in gliomas. E Cis and trans effects of significantly amplified genes (y axis) on RNA and protein level (x axis). F Kaplan–Meier curves for OS based on the mutational status of EGFR (log-rank test, WT: n = 69; EGFR^Mut: n = 6; EGFR^Amp: n = 98; EGFR^Amp&Mut: n = 14). G The bar plot showed the Ki67 positive cell percentage across patients with different EGFR mutational status (WT: n = 69; EGFR^Mut: n = 6; EGFR^Amp: n = 98; EGFR^Amp&Mut: n = 14) (mean ± SD). H The 3-D scatter plot showed the proteins changed in EGFR genomic altered samples. All significantly unregaled proteins were colored in red, downregulated were colored in blue (Wilcoxon test, p < 0.05). I The systematic diagram summarizes proteins participated in growth factor-MAPK signaling pathway that were significantly altered across samples with different EGFR mutational status. Values were color coded based on their average expression among samples with different EGFR mutational status, low to high: navy to red. J The volcano plot indicated proteins associated with the expression of cell proliferation marker (MKI67). K–O Proliferation of U-87MG and U-251MG cells associated with various treatments (n = 5 repeats per group) (mean ± SEM). P Proliferation of PDCs associated with various treatments (n = 4 repeats per group) (mean ± SEM). Q–R Tumor growth curves (n = 3 repeats per group) (mean ± SEM) (Q) and xenograft tumor images (R) of U-87MG cells subcutaneously injected into nude mice. For plot A, D and J, the two-sided Cox p value and the hazard ratio (HR) were calculated using the Cox PH model. Source data are provided as Source Data files.